Conformational dynamics plays a fundamental role in the regulation of molecular recognition and statistical mechanics provides the framework to derive a comprehensive theory for the binding free energy of a ligand to a protein. Our goal is to develop models of sufficient accuracy to be predictive for thermodynamic and kinetic properties, but also as important, to generate qualitative insights about the molecular mechanisms for binding and allosteric conformational transitions. We have three specific aims: (1) to develop new methods based on principles of statistical mechanics and molecular simulations for mapping the complex landscapes for protein conformational transitions and ligand binding. Working with our collaborators we will use these methods to (2) determine the structural basis for kinase family selectivity and regulation by small molecules, and (3) to determine the allosteric basis for inhibition of HIV-1 proteins and mechanisms of drug resistance. 1. Mapping Complex Landscapes for Protein Conformational Transitions and Ligand Binding We have established our novel physics based binding free energy model (BEDAM) as the top one for predicting binding on a scale of many dozens to a few hundred ligands to a receptor. We describe new adaptive sampling schemes based on replica exchange and Markov State Models, in order to organize, quantify and visualize the free energy landscapes and pathways on these landscapes for the projects which are the focus of specific aims two and three. Our effective potential development work is based on the AGBNP2 implicit solvent model. We will continue to work with both implicit and explicit solvent representations through the development of a new thermodynamic cycle which uses the best of both representations. 2. The Structural Basis for Kinase Selectivity and Regulation by Small Molecules The human kinome encodes about 518 kinases (PKs) which constitute one of the largest class of genes. Progress in kinase structural biology offers a conceptual framework for understanding many aspects of kinase biology. With our collaborators at the Fox Chase Cancer Center we are working on biophysical simulation and evolutionary sequence based approaches to rationalize biochemical profiling studies of kinases and to devise a framework for understanding the molecular mechanisms of selectivity of kinase inhibitors to their targets. We will address this problem from both a ligand centric and kinase centric perspective. 3. Allosteric Basis for Inhibition of HIV-1 Proteins and Mechanisms of Drug Resistance With our collaborators at the Scripps Research Institute and Ohio State University we are working on structure based inhibitor design and the acquisition of resistance to inhibitors of HIV-1 integrase and protease. We will use binding free energy and other simulation methods to analyze the basis for inhibition of allosteric integrase inhibitors which bind at the integrase core domain (CCD) dimer interface and occupy the binding pocket of the LEDGF cofactor binding site. We will work with a new class of protease inhibitors discovered by our Scripps collaborators that bind at the so called protease exo-site. We will work with our collaborators to develop effective potentials that can incorporate the effects of solvation and waters bound at the receptors in ways that are well motivated physically, fast to compute, and accurate in the sense of discriminating the correct from incorrect binding pose.